Naruto: Mutant Academy Book 1
by gorutovssageta
Summary: Naruto is sent to Xavier's school to learn how to master the Kyuubi. Naruto finds himself in a hate filled world, and vows to change their ways. But with Magneto, the Akatsuki, and humans after him can her truly make a difference? Pairings, not decided.
1. Chapter 1

_New fanfiction and I got to say I'm really excited about this one! What do you get when you combine the Astonishing X-Men with Naruto Shippuden? You get the ultimate crossover, which I shall be writing! OK, few warning before we begin the story. One, this is a Naruto based story, Naruto will be the only person to join up with the X-Men, no other shinobi shall be joining. Two, I will not be going by any of the current X-Men stories; I will be creating a team of X-Men from a roster that I'm going to create. It will consist of past and present members, such as Wolverine, Cyclops, etc. I will also be having Deadpool join the X-Men on a probationary period, he might not stay, but he might. The team of X-Men shall be this_

_Members_

_Cyclops (Leader)_

_Wolverine _

_Angel_

_Emma Frost_

_Ice-Man_

_Shadowcat_

_Marvel Girl/Phoenix _

_Beast_

_Storm_

_Nightcrawler_

_Reserve Members_

_Deadpool_

_Domino_

_X-23_

_Rogue_

_Naruto_

_OK, so that will be the line-up, so please enjoy X-Men: Naruto's Origins. This will be the first fanfiction of a three part series I will be creating. So once again, please enjoy! I do not own X-Men or Naruto. _

Chapter 1: The Professor and the Kyuubi

The morning sun shined brightly within the clear blue sky as the citizens of Konoha wandered around the shopping area, getting their early morning shopping done for the day. As this occurred, three unidentified people entered the village gates, seemingly looking for someone or something. As they entered, people watched curiously as their eyes followed the three people to the Hokage's office, where inside Shizune was desperately trying to awaken Tsunade Senju, the Hokage, or leader of the village.

"Lady Tsunade, the guests will be arriving soon, you must wake up!" Shizune shouted as she pulled on the lady Hokage's arm to pull her out of bed.

"Shizune, leave me the hell alone!" Tsunade roared sleepily as she rubbed her temples in annoyance. As much as she loved this village, being Hokage wasn't easy, especially if you had what professionals might call a drinking and gambling problem. Tsunade had spent the previous night drinking sake and gambling down in the village square, so she wasn't in the mood to be awakened. But she knew that this meeting was important, perhaps one of the most important meeting that ever occurred within the village. Naruto Uzumaki, one of the most known shinobi within the village, was being forced to leave the village due to the decision of the five nations. Even after the defeat of Pain/Nagato at the boy's hands, the nations were still in agreement that Naruto needed to receive more training to control the Kyuubi sealed within his body. After the death of his sensei Jiraiya, they believe it would be for the good of the village if Naruto receives training somewhere that the Akatsuki, a group of criminals that are after the Kyuubi within him, cannot find him. So it was suggested that they ask for the help of a world renowned professor that leads a school that can help gifted individuals learn to harness and control their abilities. The problem was that the school was in America, somewhere that was far from the village. Tsunade completely disagreed with this, but she was being outnumbered by the other nations. The votes were in, four in agreement, one in disagreement. So Tsunade sighed and allowed herself to be pulled up by Shizune, dressed, and placed within her seat at her desk. As Tsunade prepared to pull out another drink to calm her nerves, a knock was heard at the door.

"Enter…" Tsunade mumbled as a bald man entered the room within a wheelchair. He was wheeled in by a ferocious looking man, the man having long jet black hair and animal looking features. Another man entered as well, wearing strange glasses on his face.

"Excuse me, are you the leader of this village?" the bald man asked, Tsunade nodding in response. "Hello, I am Professor Charles Xavier and these are my associates Logan and Scott Summers."

"Welcome to our village sir," Shizune said warmly as she bowed in respect. "Would you like anything to drink?"

"I'm good," Logan answered roughly as Scott shook his head no.

"If you have any tea, that would be marvelous," Xavier answered as Shizune nodded and went to get the drink. "Now, I understand that this new pupil you wish me to enroll is different. I wish to understand how."

"Naruto is different, but he isn't like the normal students you might take," Tsunade explained as she looked directly at Xavier. "Naruto is what is considered as a jinchuriki in this village, meaning he has a tailed beast sealed within his body. This gives him unnatural abilities, more strength, and a higher level of chakra. At first, he was hated by many because of this, but with hard work and determination, he has overcome this obstacle. He is loved within this village as the village's champion."

"He seems like an extraordinary young man," Xavier commented as a smile crossed his face. "You see, at my school many of my students are faced with this exact problem every day, and many of them are not willing to take the route that Naruto did. They are ridiculed and hated because of the powers and abilities they possessed, labeled not normal because of them. I think that this Naruto could help us with our cause greatly if he is allowed to come to my school."

"He has no choice in the matter actually," Tsunade answered grimly as she turned away. "Naruto is being forced to leave by the other nations, so he must leave with you as soon as possible."

"That is unfortunate," Xavier answered sadly, shaking his head in disappointment. "I wish the boy didn't have to come this way…"

"So where is the kid?" Logan interrupted as he looked around the office. "We ain't got all day lady. The less time I gotta stay in this dump the better."

"Logan!" Scott shouted as Logan looked away, grumbling under his breath. "Can you have some type of respect for this village and their people?"

"Ain't my job bub," Logan answered as Scott looked at him menacingly. "You got a problem with that Summers? We can always settle it like men…" As Logan said this, he held out his right hand, three adamantium claws sliding from the middle of his knuckles. Tsunade gasped in surprise as she witnessed this, not knowing what type of ability or jutsu this was.

"That is enough Logan," Xavier said sternly, Logan sliding the claws back as he looked away in dismay. "I'm terribly sorry about Logan, he can be a bit rough sometimes. As you can see by his display, we are not normal people Lady Tsunade. This isn't one of your jutsu."

"How did you know I was thinking that?" Tsunade asked as Xavier smiled mysteriously.

"_Because I am a telepath my dear," _Xavier thought, Tsunade hearing this within her own mind. _"I can read all of your thoughts and even speak to you like this. I can do other things, but I would rather not display them now. We are what are called mutants, beings that were born with different abilities than normal humans." _

"_Mutants?" _Tsunade thought back, a startled expression crossing on her face. As Tsunade opened her mouth to speak, Naruto body flickered into the room, smoke covering the room as he stood in the middle of Xavier and Tsunade's desk.

"I'm reporting as you commanded Granny," Naruto grumbled unhappily, closing his eyes as he looked down at the ground.

"So you're the famous Naruto that I have heard so much about," Xavier said as he rolled himself to Naruto. "I'm Charles Xavier, and I have come here to help you friend. You might not be like my usual students, but you definetly fit the category. I would like to formally invite you to join us back to the Xavier Academy for Gifted Individuals."

"What choice do I have in the matter?" Naruto asked loudly, Tsunade looking at Naruto sympathetically. "I saved the village and I'm still getting tossed out of it. Whatever, I just don't care anymore. No more dreams of Hokage, just take me away so I can live my miserable life…"

"That is enough Naruto!" Tsunade interrupted as she sat up from her seat. "I know how you feel Naruto, I feel the same way as you right now! You saved the village and the council still decides that you aren't able to stay in the village? But what can we do Naruto? I need you to stay positive as I try to get the council and the nations to reconsider the decision. But I need you to give up on yourself!" Naruto looked at Tsunade with widened eyes as tears rolled down his cheek.

"I'll miss you Granny Tsunade," Naruto mumbled as he rushed up to her and wrapped her in a hug, Tsunade smiling as she returned the hug.

"Naruto, I promise I will get you back here as soon as possible," Tsunade promised as she hugged him tightly. "The council is still thinking the way that Danzo did when I was out of commission. Don't worry though, I will overturn this." Naruto nodded as he turned back to Xavier and wiped the tears from his eyes.

"OK, I'm ready to go with you," Naruto said as Xavier nodded.

"Bout time kid, let's go," Logan muttered as he stormed out the office. "Place is giving me allergies…"

"I seriously apolgize about Logan, he is just not a people person," Scott said to Tsunade as she nodded. "Thank you for allowing us here."

"I will keep you posted Lady Tsunade," Xavier said as Scott wheeled him out of the office. "Come Naruto, our jet is not too far from the village." Naruto turned back to Tsunade and waved, Tsunade waving back as Naruto walked out the office. As Naruto walked outside, he was shocked when he spotted half the village waiting outside, all with banner that said goodbye. Naruto's eyes welled up with tears again as Sakura and Kakashi stepped up and smiled warmly, wrapping Naruto in a hug as he smiled brightly.

"Don't worry Naruto, you'll be back with us soon," Sakura said as tears went down her face. "Just be careful OK? I made you some food pills in case you feel like training when you are out there OK?" Naruto nodded as she handed him a basket filled with food pills, Kakashi handing him a kunai.

"This is a special kunai, so keep it wherever you go OK?" Kakashi said as Naruto nodded. "Good luck out there Naruto."

"Wait, Naruto!"

Naruto looked back as Neji, Rock Lee, and Ten-Ten came running to him, all holding gifts.

"Here, this is some styles of training that you can work on while your there," Neji said as he handed him scrolls. "They are Hyuga family techniques, so handle them with great care." Naruto smiled as Rock Lee handed him more scrolls.

"These are some of the best taijutsu techniques that you got to learn Naruto!" Rock Lee exclaimed as he gave Naruto a salute. "Learn them and come back and show me OK?"

"And here are some ninja tools that can help you," Ten-Ten said as she handed him a pouch.

"It's time to go son," Xavier said as he placed his hand on Naruto's shoulder. "I hate to rush you, but we need to get back." Naruto nodded as he followed them out of the village, looking back one more time as everyone waved and cried behind him.

_OK, prepare for mutant and shinobi! Be back soon!_

_gorutovssageta_


	2. Chapter 2

"This is the place where we shall split up my young friend," Xavier announced as the young shinobi Naruto looked back at the mutant professor with a confused look. "I'm afraid I still have a bit of paperwork to finish back at the village, so I shall leave you in the capable hand's of Logan while Scott and I make our leave. Good luck, and be careful."

"Um, thank you?" Naruto answered, unable to comprehend why the professor would wish him "good luck" for. "Where are we going by the way?"

"Back to the X-Jet, we parked it right through this forest," Logan responded as he motioned for Naruto to follow. "Come on bub, I ain't got all day. I wanna get out this dump as soon as possible."

"Right, let's go!" Naruto exclaimed as he followed Logan into the Forest of Death. As the ventured into the perplexing forest, Naruto's paranoia increased the further he traveled.

"What's wrong with you kid?" Logan asked Naruto as he glanced at the blond haired shinobi. "Pick it up, we ain't got all night. You seem as if you've seen a ghost."

"I think we're being followed," Naruto answered as he scanned the area. "Someone is around here, I swear it... wait. who is...?" Naruto was bombarded in an array of bullet's, the shinobi using the Substitution Jutsu to escape any damage.

"Oh yeah, Deadpool has found the new guy babe!" a voice roared as a man dressed in a red and black jumpsuit with two katanas laced on his back teleported in front of Logan. "Heeey, where did new guy go? I know you saw him John Wayne, so spill the coffee!" Logan only growled as three adamantium claws slid from between each of his knuckles.

"You got something to say to me punk?" Logan asked as the man sneered in response. "Or do you just got a death wish? Either way, it's time to pay the piper."

"Hey, I might owe a lot of money to people, but I never owed anyone name Piper money!" the man spat back. "Well, maybe I did during those Vegas nights. But do you think I remember those, I THINK NOT!" Logan only grunted as he took a swing at the man's head, but the man teleported to the back of Logan, unsheathing his katana. As he prepared to lodge the sword into Logan's back, Naruto appeared from a tree, kicking the katana from the man's hand. He then followed up with a punch to the man's jaw, who simply swayed from the blow as it entered his radius.

"Oh, too slow ninja boy!" the man shouted as he kicked Naruto in the chest, causing the shinobi to go into a tree positioned behind him. As Naruto's back hit the tree, the boy disappeared in a cloud of smoke.

"What's going on, you got any visual Domino?" the man asked in a hidden mic on his suit, which signaled to a girl who was hidden in a tree in a disclosed location. She watched the battle through a pair of binocular's, but was unable to pick up the boy's location.

"You lost the target Deadpool, like usual," Domino responded as she sighed. "Can't you ever be serious for once? We're supposed to be in a training session, so if you screw this up, Scott is going to kill you."

"Let him, I just came along for the popcorn!" Deadpool joked as he glanced back at Logan, who was waiting impatiently.

"Aren't you supposed to "defeat" me idiot?" Logan whispered to the Merc with a Mouth, who jumped up in response.

"Oh right, let's finish this off!" Deadpool shouted as he pulled a gun from a holster on his belt, taking a shot right at Logan's head, which caused the X-Man to fall to the ground. "That should do it! Now you're all alone kid! No one is here to save you, so come on out!"

"Wait, I'm sensing brain wave pattern's that seem to be going haywire in an area right in your radius Deadpool." another woman stated as Deadpool sighed.

"Oh, now the psychic on the team want's to put in her 5 cent," Deadpool responded as an angry Naruto emerged from the tree. But not just one, over a hundred.

"He's being outnumbered, let's jump in the fight!" Domino shouted as the other woman sighed.

"Fine, but don't you do anything stupid, this is a training session," the woman answered as Domino entered the battlefield, a sniper rifle on her back. "X-Men, attack!" Each X-Men that was posted in the area appeared, starting with the woman who was feeding Domino and Deadpool information.

"Emma, nice us you to join our party!" Deadpool shouted as the woman named Emma nodded as she went into battle. Next, was a blue skinned individual who teleported in from the X-Jet, taking out at least two Naruto's as he made his appearance.

"Good Nightcrawler, these are just duplicate's, but their like flesh and blood!" Emma shouted as she sent an attacking Naruto back with a psi-wave. Next was a white haired woman, who flew in from the sky, sending down lightning bolt's at the shinobi.

"Bring in the storm Storm!" Deadpool shouted as the woman named Storm ignored him. As the number of clones dwindled, Naruto gathered chakra in his left palm for a Rasengan, charging it right into Deadpool, who had entered his radius. Deadpool was sent flying as the remaining clones were dismantled by an unknown force, who seemed to be finishing them off with claws... Naruto could only blink as a girl around his age stood before him, her black hair flowing in the breeze. She had a determined look on her face, one that said she would never give in, no matter the cause. Naruto grinned as he cracked his knuckles, running at the girl at full speed as the girl responded in the same manner. As he ran, Naruto sent a kunai at the girl's chest, which was rejected by her as she sliced it in half as it entered her radius via two sharp adamantium claws. Naruto sent several more at her, the result the same each time. As they neared each other's radius, Naruto went on the offensive, unleashing a tail of chakra, which enveloped his body in the Kyuubi no Yoko's chakra. The girl was surprised, but this did not slow her down. She advanced forward, sending mean uppercut Naruto's way, which the shinobi dodged. They began to exchange blows, everyone else in the area watching as they allowed the girl and Naruto to be isolated. Naruto used his own chakra claws to keep up with the girl's fierce claws, keeping the two slightly on par. Each blow was precise and deadly; The girl was no amateur in the art of battle, which Naruto picked up very quickly. She wouldn't make a mistake, so it was up to the shinobi to force her out of her comfort zone. Naruto allowed himself to be attacked, using the Substitution Jutsu to evade any injury. As the girl scanned the area, Naruto stood in a tree, pulling out a large scroll that was given to him by Ten-Ten. He made the corresponding hand signs, summoning several ninja tools. He then used the Kage Bushin no Jutsu (Multi Shadow Clone Jutsu) which he sent his clones to be positioned in a tree, each with their own weapon. The girl began to sniff the air, locating the Naruto who was doing the jutsu in the tree. She ran to the tree, and without warning she cut it down with a quick swipe of her claw. The tree toppled over, Naruto jumping down as Emma used her psychic abilities to keep the tree at bay.

"Be careful Laura, don't kill the boy," Emma warned as the girl Laura nodded. Each of the Naruto's positioned in the trees attacked from each direction, Laura going into the defensive as she kicked one away, allowed two to collide into each other by ducking, then stabbed one in the chest with one quick movement. As she turned around, she was greeted by the real Naruto, who held a Odama Rasengan in his palm. He slammed his mighty Rasengan into Laura's chest, the girl letting out a moan as her chest was drilled into. She collapsed, Naruto preparing to take on the other X-Men as another pair of claws were held at his neck.

"Show's over bub, you passed," Logan stated as Naruto turned around, befuddled. "We don't usually do this with all our soon to be's, but Chuck said you are already a seasoned fighter, so he wanted to see how you did in a combat situation."

"I must say, I was quite impressed," Xavier announced as he appeared out of nowhere, Naruto looking at the professor in shock. "Yes, I was here all along my friend. You are quite the spectacle, being able to control such vast power so easily. I sense you did not use even half of your potential there, which is astounding as you beat Laura, who is one of our star pupil's in the Academy."

"Yeah, pretty damn sloppy kid, letting yourself get beat by a newbie," Logan scowled as Laura looked down in disappointment. "Alright, let's get back to the jet, I'm tired and want a beer."

"Yes, let us go," Xavier added as Naruto followed the X-Men, still a bit confused, but somewhat eager to see what would happen next.

_OK, second chapter of Naruto: Mutant Academy! Sorry that took FOREVER, but it's been a looooooooong semester. So keep reading, and I'll give you the goods! gorutovssageta, out! _

_gorutovsageta_


End file.
